Levin, L. A. et al. The function of marine critical transition zones and the importance of sediment biodiversity. Ecosystems 4, 430–451 (2001).
Google Scholar
Sarathchandra, C. et al. Significance of mangrove biodiversity conservation in fishery production and living conditions of coastal communities in Sri Lanka. Diversity 10, 20 (2018).
Google Scholar
Brown, C. J. et al. The assessment of fishery status depends on fish habitats. Fish Fish. 20, 1–14 (2019).
Google Scholar
Kathiresan, K. & Bingham, B. L. Biology of mangroves and mangrove ecosystems. Adv. Mar. Biol. 40, 84–254 (2001).
De La Morinière, E. C., Pollux, B., Nagelkerken, I. & Van der Velde, G. Post-settlement life cycle migration patterns and habitat preference of coral reef fish that use seagrass and mangrove habitats as nurseries. Estuar. Coast. Shelf Sci. 55, 309–321 (2002).
Google Scholar
Asaad, I., Lundquist, C. J., Erdmann, M. V. & Costello, M. J. Delineating priority areas for marine biodiversity conservation in the Coral Triangle. Biol. Conserv. 222, 198–211 (2018).
Google Scholar
Myers, N., Mittermeier, R. A., Mittermeier, C. G., Da Fonseca, G. A. & Kent, J. Biodiversity hotspots for conservation priorities. Nature 403, 853 (2000).
Google Scholar
Chong, V. C., Lee, P. K. & Lau, C. M. Diversity, extinction risk and conservation of Malaysian fishes. J. Fish Biol. 76, 2009–2066. https://doi.org/10.1111/j.1095-8649.2010.02685.x (2010).
Google Scholar
Wong, S. L. Matang Mangroves: A Century of Sustainable Management (Sasyaz Holdings Private Ltd., Forestry Department Peninsular Malaysia, 2004).
Ong, J. et al. Hutan paya laut Merbok, Kedah: Pengurusan hutan, persekitaran fizikal dan kepelbagaian flora. In Siri Kepelbagaian Biologi Hutan Vol. 23 (eds Ku-Aman, K. A. et al.) 21–33 (Jabatan Perhutanan Semenanjung Malaysia, 2015).
Jamaluddin, J. A. F. et al. DNA barcoding of shrimps from a mangrove biodiversity hotspot. Mitochondrial DNA Part A 30, 618–625. https://doi.org/10.1080/24701394.2019.1597073 (2019).
Google Scholar
Mansor, M., Mohammad-Zafrizal, M., Nur-Fadhilah, M., Khairun, Y. & Wan-Maznah, W. Temporal and spatial variations in fish assemblage structures in relation to the physicochemical parameters of the Merbok estuary, Kedah. J. Nat. Sci. Res. 2, 110–127 (2012).
Hookham, B., Shau-Hwai, A. T., Dayrat, B. & Hintz, W. A baseline measure of tree and gastropod biodiversity in replanted and natural mangrove stands in Malaysia: Langkawi Island and Sungai Merbok. Trop. Life Sci. Res. 25, 1 (2014).
Google Scholar
Mansor, M., Najamuddin, A., Mohammad-Zafrizal, M., Khairun, Y. & Siti-Azizah, M. Length-weight relationships of some important estuarine fish species from Merbok estuary, Kedah. J. Nat. Sci. Res. 2, 8–19 (2012).
Zainal Abidin, D. H. et al. Ichthyofauna of Sungai Merbok Mangrove Forest Reserve, northwest Peninsular Malaysia, and its adjacent marine waters. Check List 17, 601–631 (2021).
Google Scholar
Lim, H. C., Zainal Abidin, M., Pulungan, C. P., de Bruyn, M. & Mohd Nor, S. A. DNA barcoding reveals high cryptic diversity of the freshwater halfbeak genus Hemirhamphodon from Sundaland. PLoS ONE 11, e0163596 (2016).
Google Scholar
Mennesson, M. I., Bonillo, C., Feunteun, E. & Keith, P. Phylogeography of Eleotris fusca (Teleostei: Gobioidei: Eleotridae) in the Indo-Pacific area reveals a cryptic species in the Indian Ocean. Conserv. Genet. 19, 1025–1038 (2018).
Google Scholar
Gomes, L. C., Pessali, T. C., Sales, N. G., Pompeu, P. S. & Carvalho, D. C. Integrative taxonomy detects cryptic and overlooked fish species in a neotropical river basin. Genetica 143, 581–588 (2015).
Google Scholar
Iyiola, O. A. et al. DNA barcoding of economically important freshwater fish species from north-central Nigeria uncovers cryptic diversity. Ecol. Evol. 8, 6932–6951 (2018).
Google Scholar
Stern, N., Rinkevich, B. & Goren, M. Integrative approach revises the frequently misidentified species of Sardinella (Clupeidae) of the Indo-West Pacific Ocean. J. Fish Biol. 89, 2282–2305 (2016).
Google Scholar
Hebert, P. D., Ratnasingham, S. & De Waard, J. R. Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. Lond. Ser. B Biol. Sci. 270, S96–S99 (2003).
Google Scholar
Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R. & Hebert, P. D. DNA barcoding Australia’s fish species. Philos. Trans. R. Soc. B Biol. Sci. 360, 1847–1857 (2005).
Google Scholar
Xu, L. et al. Assessment of fish diversity in the South China Sea using DNA taxonomy. Fish. Res. 233, 105771 (2020).
Google Scholar
Lakra, W. et al. DNA barcoding Indian marine fishes. Mol. Ecol. Resour. 11, 60–71 (2011).
Google Scholar
Hubert, N. et al. Cryptic diversity in Indo-Pacific coral-reef fishes revealed by DNA-barcoding provides new support to the centre-of-overlap hypothesis. PLoS ONE 7, e28987 (2012).
Google Scholar
Adibah, A. & Darlina, M. Is there a cryptic species of the golden snapper (Lutjanus johnii)?. Genet. Mol. Res. 13, 8094–8104 (2014).
Google Scholar
Bakar, A. A. et al. DNA barcoding of Malaysian commercial snapper reveals an unrecognized species of the yellow-lined Lutjanus (Pisces: Lutjanidae). PLoS ONE 13, e0202945 (2018).
Google Scholar
Farhana, S. N. et al. Exploring hidden diversity in Southeast Asia’s Dermogenys spp. (Beloniformes: Zenarchopteridae) through DNA barcoding. Sci. Rep. 8, 1–11 (2018).
Jaafar, T. N. A. M., Taylor, M. I., Nor, S. A. M., de Bruyn, M. & Carvalho, G. R. DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes). PLoS ONE 7, e49623 (2012).
Google Scholar
Azmir, I., Esa, Y., Amin, S., Salwany, M. & Zuraina, M. DNA barcoding analysis of larval fishes in Peninsular Malaysia. J. Environ. Biol. 41, 1295–1308 (2020).
Google Scholar
Chu, C. et al. Using DNA barcodes to aid the identification of larval fishes in tropical estuarine waters (Malacca Straits, Malaysia). Zool. Stud. 58, e30 (2019).
Google Scholar
Hubert, N., Delrieu-Trottin, E., Irisson, J.-O., Meyer, C. & Planes, S. Identifying coral reef fish larvae through DNA barcoding: A test case with the families Acanthuridae and Holocentridae. Mol. Phylogenet. Evol. 55, 1195–1203 (2010).
Google Scholar
Ko, H.-L. et al. Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding. PLoS ONE 8, e53451 (2013).
Google Scholar
Chin, T. C., Adibah, A., Hariz, Z. D. & Azizah, M. S. Detection of mislabelled seafood products in Malaysia by DNA barcoding: Improving transparency in food market. Food Control 64, 247–256 (2016).
Google Scholar
Hubert, N. et al. Identifying Canadian freshwater fishes through DNA barcodes. PLoS ONE 3, e2490 (2008).
Google Scholar
Landi, M. et al. DNA barcoding for species assignment: The case of Mediterranean marine fishes. PLoS ONE 9, e106135 (2014).
Google Scholar
Russell, D., Thuesen, P. & Thomson, F. A review of the biology, ecology, distribution and control of Mozambique tilapia, Oreochromis mossambicus (Peters 1852) (Pisces: Cichlidae) with particular emphasis on invasive Australian populations. Rev. Fish Biol. Fish. 22, 533–554 (2012).
Google Scholar
Hebert, P. D., Cywinska, A. & Ball, S. L. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B Biol. Sci. 270, 313–321 (2003).
Google Scholar
Puillandre, N., Lambert, A., Brouillet, S. & Achaz, G. ABGD, automatic barcode gap discovery for primary species delimitation. Mol. Ecol. 21, 1864–1877 (2012).
Google Scholar
Meier, R., Zhang, G. & Ali, F. The use of mean instead of smallest interspecific distances exaggerates the size of the “barcoding gap” and leads to misidentification. Syst. Biol. 57, 809–813 (2008).
Google Scholar
Ortiz, D. & Francke, O. F. Two DNA barcodes and morphology for multi-method species delimitation in Bonnetina tarantulas (Araneae: Theraphosidae). Mol. Phylogenet. Evol. 101, 176–193 (2016).
Google Scholar
Hajibabaei, M., Singer, G. A., Hebert, P. D. & Hickey, D. A. DNA barcoding: How it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet. 23, 167–172 (2007).
Google Scholar
Mecklenburg, C. W., Møller, P. R. & Steinke, D. Biodiversity of arctic marine fishes: taxonomy and zoogeography. Mar. Biodivers. 41, 109–140 (2011).
Google Scholar
Puckridge, M., Andreakis, N., Appleyard, S. A. & Ward, R. D. Cryptic diversity in flathead fishes (Scorpaeniformes: Platycephalidae) across the Indo-West Pacific uncovered by DNA barcoding. Mol. Ecol. Resour. 13, 32–42 (2013).
Google Scholar
Thirumaraiselvi, R. & Thangaraj, M. Genetic diversity analysis of Indian Salmon, Eleutheronema tetradactylum from South Asian countries based on mitochondrial COI gene sequences. Not. Sci. Biol. 7, 417–422 (2015).
Google Scholar
Delrieu-Trottin, E. et al. Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo-Australian Archipelago through the iterative use of DNA-based species delimitation and specimen assignment methods. Evol. Appl. 13, 1451–1467 (2020).
Google Scholar
Durand, J.-D., Hubert, N., Shen, K.-N. & Borsa, P. DNA barcoding grey mullets. Rev. Fish Biol. Fish. 27, 233–243 (2017).
Google Scholar
Alavi-Yeganeh, M. S., Khajavi, M. & Kimura, S. A new ponyfish, Deveximentum mekranensis (Teleostei: Leiognathidae), from the Gulf of Oman. Ichthyol. Res. 68, 437–444. https://doi.org/10.1007/s10228-020-00794-y (2021).
Google Scholar
Carpenter, K. E. & Niem, V. FAO Species Identification Guide for Fishery Purposes. The Living Marine Resources of the Western Central Pacific. Bony Fishes Part 4 (Labridae to Latimeriidae), Estuarine Crocodiles, Sea Turtles, Sea Snakes and Marine Mammals Vol. 6 (FAO Library, 2001).
Chen, W., Ma, X., Shen, Y., Mao, Y. & He, S. The fish diversity in the upper reaches of the Salween River, Nujiang River, revealed by DNA barcoding. Sci. Rep. 5, 1–12 (2015).
Guimarães-Costa, A. J. et al. Fish diversity of the largest deltaic formation in the Americas-a description of the fish fauna of the Parnaíba Delta using DNA Barcoding. Sci. Rep. 9, 1–8 (2019).
Google Scholar
Hupało, K. et al. An urban Blitz with a twist: Rapid biodiversity assessment using aquatic environmental DNA. Environ. DNA 3, 200–213 (2020).
Google Scholar
Zainal Abidin, D. H. & Noor Adelyna, M. A. Universities as Living Labs for Sustainable Development 211–225 (Springer, 2020).
Ratnasingham, S. & Hebert, P. D. BOLD: The barcode of life data system. Mol. Ecol. Notes 7, 355–364 (2007).
Google Scholar
Benson, D. A. et al. GenBank. Nucleic Acids Res. 46, D41–D47 (2018).
Google Scholar
Mansor, M. I. et al. Field Guide to Important Commercial Marine Fishes of the South China Sea (SEAFDEC/MFRDMD, 1998).
Nuruddin, A. A. & Isa, S. M. Trawl Fisheries in Malaysia-Issues, Challenges and Mitigating Measures (Fisheries Research Institute, Department of Fisheries Malaysia, 2013).
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
Google Scholar
Kimura, M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111–120 (1980).
Google Scholar
Bouckaert, R. et al. BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 10, e1003537 (2014).
Google Scholar
Edler, D., Klein, J., Antonelli, A. & Silvestro, D. raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML. Methods Ecol. Evol. 12, 373–377 (2021).
Google Scholar
Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T. & Calcott, B. PartitionFinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol. Biol. Evol. 34, 772–773 (2017).
Google Scholar
Miller, M. A., Pfeiffer, W. & Schwartz, T. In Proceedings of the 2011 TeraGrid Conference: Extreme digital discovery 1–8 (2011).
Rambaut, A. FigTree v1.4.4. Available from: http://tree.bio.ed.ac.uk/software/figtree/ (2018).
Ratnasingham, S. & Hebert, P. D. A DNA-based registry for all animal species: The Barcode Index Number (BIN) system. PLoS ONE 8, e66213 (2013).
Google Scholar
Pons, J. et al. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst. Biol. 55, 595–609 (2006).
Google Scholar
Glez-Pena, D., Gomez-Blanco, D., Reboiro-Jato, M., Fdez-Riverola, F. & Posada, D. ALTER: Program-oriented conversion of DNA and protein alignments. Nucleic Acids Res. 38, W14–W18 (2010).
Google Scholar
Team, R. RStudio: integrated development for R (RStudio Inc., 2015).
Fujisawa, T. & Barraclough, T. G. Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: A revised method and evaluation on simulated data sets. Syst. Biol. 62, 707–724 (2013).
Google Scholar
Source: Ecology - nature.com